Synapse Manual Updated 2021-09-28 Synapse Manual | 2 © 2016-2021 Tucker-Davis Technologies, Inc. (TDT). All rights reserved. Tucker-Davis Technologies 11930 Research Circle Alachua, FL 32615 USA Phone: +1.386.462.9622 Fax: +1.386.462.5365 Notices The information contained in this document is provided "as is," and is subject to being changed, without notice. TDT shall not be liable for errors or damages in connection with the furnishing, use, or performance of this document or of any information contained herein. The latest versions of TDT documents are always online at https://www.tdt.com/docs/ Table of Contents | 3 Table of Contents Synapse: Next Generation Performance Today Design 6 Manage 11 Collect 12 Next Generation Performance Today 13 Getting Started with Synapse Before You Begin 15 Launching Your First Experiment 20 Using Gizmos to Build an Experiment 33 Managing Data for Your Lab 41 Managing Users and Subjects 46 Synapse Fundamentals Reference Hardware Configuration 55 Designtime Reference 62 Runtime 85 Hardware Reference Hardware Reference 92 RZ and RX Processors 93 LR10 Lab Rat Interface Module 101 Data Streamers 112 RZ-UDP Interface 115 Video Processors 118 Subject Interface Amplifiers 124 PZ Amplifiers 133 RA Amplifiers 144 Subject Interface Stimulation 146 IZ2 Electrical Stimulation 155 iCon Behavioral Control Interface 158 iH10 High Voltage Interface 169 iN10 High Voltage Interface 172 iL24 Digital Logic Interface 175 iR5 IR Driver Interface 178 iM10 Multi-Function Interface 181 BH32 Behavioral Controller Interface 190 Gizmo Reference Gizmo Reference 193 Table of Contents | 4 Gizmo Categories 196 Using Parameters 206 Creating User Gizmos 214 Artifact Blocker 220 Audio Stimulation 226 Box Spike Sorting 239 Delay 252 Electrical Stim Driver 256 Electrical Stimulation 269 Epoch Event Storage 278 Fiber Photometry for RZ10 Processor 281 Fiber Photometry for non-RZ10 Processors 297 File Stimulation 309 General Purpose Filter 321 Injector 324 Local Field Potentials (LFP) 330 Mapper 334 Merger 340 MRI Recording Processor 342 Neural Signal Referencer 348 Neural Stream Processor 355 Oscilloscope 361 Parameter Manifold 371 Parameter Sequencer 380 PCA Spike Sorting 392 Pulse Generator 406 Pulse Train Generator 412 Python Coding Gizmo 421 Selector 422 Signal Accumulator 428 Sort Binner 437 State Maker 442 Stream Data Storage 450 Strobed Data Storage 453 Tetrode Spike Sorting 462 Timer 483 Ultrasonic Stimulation 493 Unary Signal Processor 502 User Input 510 Table of Contents | 5 Synapse Training Videos Synapse Suite 516 Lab Rat and Synapse Lite 526 Miscellanous 528 Cluster Processing with Synapse Overview 529 Setting Up Cluster Computing 530 Hardware Configuration 531 The Rig 533 Processing Tree 535 Preferences 537 Troubleshooting FAQs Investigating a Synapse Crash 545 Remote Experiment Design Overview 552 Installing TDT Drivers and Synapse on another Computer 552 Setting Up Corpus for Your Rig 553 Example Experiment 556 Using Your Own Data 558 Exporting Your Experiment to Another Computer 558 Corpus Limitations 559 How to Update Synapse Release Notes v96 562 v95 564 v94 566 v92 568 v90 571 v88 575 v86 578 Synapse: Next Generation Performance Today | 6 Synapse: Next Generation Performance Today Synapse is the software you'll use to design, manage and collect data from your neurophysiology experiments using System 3 hardware. With Synapse's advanced automation, underlying relational database, and sophisticated hardware interface; the power and flexibility of TDT's proven multi-DSP hardware platform is never more than a few clicks away. Design In the design phase of your experiment, Synapse automates all but the highest level set-up tasks. You interact with the software using a streamlined interface where the most commonly modified options are available on easy options tabs. Automated processes combine what Synapse knows about your hardware and what TDT has learned in over 30 years of working closely with researchers like you to deliver smart experiment design. Synapse: Next Generation Performance Today | 7 Let Synapse Remember the Details of Your Hardware for You Synapse auto-detects your hardware and uses a hardware abstraction layer (or HAL) between the device specific processes for your equipment and your experiment building selections. When you are configuring recording, data storage, and detection tasks; you don't have to think about the particulars of your hardware system. As you design your experiment, Synapse uses information about your hardware and selections you've already made to show only the relevant choices. You select the parts of the experiment you want and Synapse generates the required code instructions, optimized for your hardware. With only a few mouse clicks, you can build custom experiments and be collecting data in minutes. Get the Power of Customization without Complexity Most Synapse users will be able to run out-of-box experiments and acquire data with minimal configuration changes. If you need to do more, there are progressively more detailed levels of design options available. Three powerful paths can be used or combined to support differing levels of flexibility and control. Experiment Templates For the fastest design experience, select a pre-made template as the starting point for your experiment. The growing list of TDT designed templates includes multi-channel recording, LFPs, spike sorting, tetrode recordings, and experiments that combine these elements. If the template matches your needs, you can use it as is. For more customized experiments, adjust configuration settings or add gizmo task blocks to make it your own. Templates Synapse: Next Generation Performance Today | 8 TDT Gizmos For a balance of flexibility and design speed, select and arrange ready-made building blocks called 'gizmos'. You add them in the order you want each task to occur, for example you would add a filter before a storage task. Synapse adjusts the available options as you work so that only relevant choices are available. Gizmos are available for a variety of tasks, including reading input signals, filtering, online spike sorting, data storage, channel mapping, stimulation, and much more. Each gizmo can also comprise a group of tasks bundled together for a particular type of experiment, such as online spike sorting and data storage. TDT Gizmos (partial list) Many gizmos include runtime interfaces that enable you to make adjustments to your experiment as data is being collected. For example, the Tetrode Processor includes plots to display the four channels of the tetrode as streamed waveforms and as snippets in a pile plot. A specialized 2D feature plot for viewing and selecting different projections is also provided. You can draw clusters or units and apply them from the runtime interface. You can even make changes to the filter settings or threshold levels dynamically and see the changes to the data immediately. Synapse: Next Generation Performance Today | 9 Runtime Interface User Designed Gizmos For maximum flexibility and control, build your own custom processing tasks. The gizmo building tools link directly into the signal flow, and include parameter tags or 'hooks' that allow you to control timing, triggering, data storage, and modification of other parameter values dynamically at runtime. For example, you can create a gizmo that runs a novel stimulus protocol, accessing signal parameters directly in the Synapse interface or through a custom application you've developed using TDT provided development tools and MATLAB or Python. Designing your own gizmos may take a little more time upfront, but once a user gizmo has been created it can be reused in future experiments as easily as the built-ins. Synapse: Next Generation Performance Today | 10 User Designed Gizmo Creation Tools Get More from Your System with Automation No matter which method or combination of techniques you use to define your experiment, the Synapse compilation engine determines how to most efficiently utilize your available hardware to run it. One of the reasons System 3 processors are so powerful is that they run multiple DSPs in parallel. Each DSP is capable of running many combinations of tasks, but each task takes a different amount of processing power. Automating the distribution of the tasks that make up your experiment allows you to tap in to the full power of the multiple DSP architecture of the processors in your system from day one and without any special training. With Synapse, you let the computer do the logic based tasks it does so well; giving you more time to do what you do best-- consider big ideas, get creative, and develop insightful conclusions. Synapse: Next Generation Performance Today | 11 Manage Much of what makes Synapse innovative goes on behind the scenes. Like the automation tools at work as you design your experiments, the relational database is the power behind Synapse's experiment management capabilities. Synapse tags three special categories of information: users, experiments, and subjects; then tracks all runtime settings and any modification made to parameters during each experiment run. Persistence You control how Synapse uses the stored runtime configuration data by selecting a Persistence--or way of choosing how settings carryover from user to user, subject to subject, or session to session. Tagging the visual layout and runtime parameters with subject and user information gives your lab several options for customizing the experience for each user. Different users can run a shared experiment with completely different settings. Or individual users can choose to: • Use the most recent settings for that project or that subject. • Start over with a fresh interface. • Start with settings from any previous session. The Digital Lab Notebook You can access the complete record of all settings and changes made during each session in the History Window. The relational nature of the database where they're stored enables you to filter sessions in the window by user, experiment, or subject. When you select a session, you can see every change that was made to settings during each run.